Matching Items (88)
Description
A distinct characteristic of ferroelectric materials is the existence of a reversible spontaneous polarization with the application of an electric field. The relevant properties ferroelectric lithium niobate surfaces include a low density of defects and external screening of the bound polarization charge. These properties result in unique surface electric field distribution with a strong electric field in the vicinity of domain boundaries, while away from the boundaries, the field decreases rapidly. In this work, ferroelectric lithium niobate (LN) is used as a template to direct the assembly of metallic nanostructures via photo-induced reduction and a substrate for deposition of ZnO semiconducting thin films via plasma enhanced atomic layer deposition (PE-ALD). To understand the mechanism the photo-induced deposition process the following effects were considered: the illumination photon energy and intensity, the polarization screening mechanism of the lithium niobate template and the chemical concentration. Depending on the UV wavelength, variation of Ag deposition rate and boundary nanowire formation are observed and attributed to the unique surface electric field distribution of the polarity patterned template and the penetration depth of UV light. Oxygen implantation is employed to transition the surface from external screening to internal screening, which results in depressed boundary nanowire formation. The ratio of the photon flux and Ag ion flux to the surface determine the deposition pattern. Domain boundary deposition is enhanced with a high photon/Ag ion flux ratio while domain boundary deposition is depressed with a low photon/Ag ion flux ratio. These results also support the photo-induced deposition model where the process is limited by carrier generation, and the cation reduction occurs at the surface. These findings will provide a foundational understanding to employ ferroelectric templates for assembly and patterning of inorganic, organic, biological, and integrated structures. ZnO films deposited on positive and negative domain surfaces of LN demonstrate different I-V curve behavior at different temperatures. At room temperature, ZnO deposited on positive domains exhibits almost two orders of magnitude greater conductance than on negative domains. The conductance of ZnO on positive domains decreases with increasing temperature while the conductance of ZnO on negative domains increases with increasing temperature. The observations are interpreted in terms of the downward or upward band bending at the ZnO/LN interface which is induced by the ferroelectric polarization charge. Possible application of this effect in non-volatile memory devices is proposed for future work.
ContributorsSun, Yang (Author) / Nemanich, Robert (Thesis advisor) / Bennett, Peter (Committee member) / Sukharev, Maxim (Committee member) / Ros, Robert (Committee member) / McCartney, Martha (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes several approaches to next generation DNA sequencing via tunneling current method based on a Scanning Tunneling Microscope system. In chapters 5 and 6, preliminary results have shown that DNA bases could be identified by their characteristic tunneling signals. Measurements taken in aqueous buffered solution showed that single base resolution could be achieved with economic setups. In chapter 7, it is illustrated that some ongoing measurements are indicating the sequence readout by making linear scan on a piece of short DNA oligomer. However, to overcome the difficulties of controlling DNA especially ssDNA movement, it is much better to have the tunneling measurement incorporated onto a robust nanopore device to realize sequential reading of the DNA sequence while it is being translocated.
ContributorsHuang, Shuo (Author) / Lindsay, Stuart (Thesis advisor) / Sankey, Otto (Committee member) / Tao, Nongjian (Committee member) / Drucker, Jeff (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis describes several experiments based on carbon nanotube nanofludic devices and field-effect transistors. The first experiment detected ion and molecule translocation through one single-walled carbon nanotube (SWCNT) that spans a barrier between two fluid reservoirs. The electrical ionic current is measured. Translocation of small single stranded DNA oligomers is marked by large transient increases in current through the tube and confirmed by a PCR (polymerase chain reaction) analysis. Carbon nanotubes simplify the construction of nanopores, permit new types of electrical measurement, and open new avenues for control of DNA translocation. The second experiment constructed devices in which the interior of a single-walled carbon nanotube field-effect transistor (CNT-FET) acts as a nanofluidic channel that connects two fluid reservoirs, permitting measurement of the electronic properties of the SWCNT as it is wetted by an analyte. Wetting of the inside of the SWCNT by water turns the transistor on, while wetting of the outside has little effect. This finding may provide a new method to investigate water behavior at nanoscale. This also opens a new avenue for building sensors in which the SWCNT functions as an electronic detector. This thesis also presents some experiments that related to nanofabrication, such as construction of FET with tin sulfide (SnS) quantum ribbon. This work demonstrates the application of solution processed IV-VI semiconductor nanostructures in nanoscale devices.
ContributorsCao, Zhai (Author) / Lindsay, Stuart (Thesis advisor) / Vaiana, Sara (Committee member) / Ros, Robert (Committee member) / Marzke, Robert (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
Nanofluidic devices in which one single-walled carbon nanotube (SWCNT) spans a barrier between two fluid reservoirs were constructed, enabling direct electrical measurement of the transport of ions and molecules. Ion current through these devices is about 2 orders of magnitude larger than that predicted from the bulk resistivity of the electrolyte. Electroosmosis drives excess current, carried by cations, and is found to be the origin of giant ionic current through SWCNT as shown by building an ionic field-effect transistor with a gate electrode embedded in the fluid barrier. Wetting of inside of the semi-conducting SWCNT by water showed the change of its electronic property, turning the electronic SWCNT field-effect transistor to "on" state. These findings provide a new method to investigate and control the ion and molecule behavior at nanoscale.
ContributorsPang, Pei (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Shumway, John (Committee member) / Tao, Nongjian (Committee member) / Menéndez, Jose (Committee member) / Arizona State University (Publisher)
Created2011
Description
Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-atom RMSD from their experimental crystal structures. Protein evolution and disease associated mutations (DAMs) are most commonly studied by in silico multiple sequence alignment methods. Here, however, the structural dynamics are incorporated to give insight into the evolution of three ancestral proteins and the mechanism of several diseases in human ferritin protein. The differences in conformational dynamics of these evolutionary related, functionally diverged ancestral steroid receptor proteins are investigated by obtaining the most collective motion through essential dynamics. Strikingly, this analysis shows that evolutionary diverged proteins of the same family do not share the same dynamic subspace. Rather, those sharing the same function are simultaneously clustered together and distant from those functionally diverged homologs. This dynamics analysis also identifies 77% of mutations (functional and permissive) necessary to evolve new function. In silico methods for prediction of DAMs rely on differences in evolution rate due to purifying selection and therefore the accuracy of DAM prediction decreases at fast and slow evolvable sites. Here, we investigate structural dynamics through computing the contribution of each residue to the biologically relevant fluctuations and from this define a metric: the dynamic stability index (DSI). Using DSI we study the mechanism for three diseases observed in the human ferritin protein. The T30I and R40G DAMs show a loss of dynamic stability at the C-terminus helix and nearby regulatory loop, agreeing with experimental results implicating the same regulatory loop as a cause in cataracts syndrome.
ContributorsGlembo, Tyler J (Author) / Ozkan, Sefika B (Thesis advisor) / Thorpe, Michael F (Committee member) / Ros, Robert (Committee member) / Kumar, Sudhir (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
One of the most important issues in femtosecond free electron laser X-ray diraction is to reconstruct the 3D charge density of molecule from a mass of diraction snapshots. In order to determine the orientation of single molecule from diraction patterns, we rst determine the moments and products of inertia of this from 2D experiment data (diraction patterns or EM images to obtain the elements of the inertia tensor. If diraction patterns from uniformly random orientations or some preferred orientations are collected, the principal axes of the molecule can be extracted, together with the Euler angles which relate the principal axes of the molecule to the laboratory frame axes. This is achieved by nding the maximum and minimum values for the measured moments from many single-molecule patterns. Simulations for GroEL protein indicates that the calculation of the autocorrelation help eliminate the Poisson noise in Cryo- EM images and can make correct orientation determination. The eect of water jacket surrounding the protein molecule is studied based on molecular dynamics simulation result. The intensities from water and interference is found to suppress those from protein itself. A method is proposed and applied to the simulation data to show the possibility for it to overcome the water background problem. The scattering between Bragg re ections from nanocrystals is used to aid solution of the phase problem. We describe a method for reconstructing the charge density of a typical molecule within a single unit cell, if suciently nely-sampled diraction data are available from many nanocrystals of dierent sizes lying in the same orientations without knowledge of the distribution of particle size or requiring atomic-resolution data. Triple correlation of the diraction patterns are made use of to reconiii
ContributorsWang, Xiaoyu (Author) / Spence, John C.H. (Thesis advisor) / Schmidt, Kevin (Committee member) / Doak, R. Bruce (Committee member) / Weierstall, Uwe (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2011
Description
In this research, our goal was to fabricate Josephson junctions that can be stably processed at 300°C or higher. With the purpose of integrating Josephson junction fabrication with the current semiconductor circuit fabrication process, back-end process temperatures (>350 °C) will be a key for producing large scale junction circuits reliably, which requires the junctions to be more thermally stable than current Nb/Al-AlOx/Nb junctions. Based on thermodynamics, Hf was chosen to produce thermally stable Nb/Hf-HfOx/Nb superconductor tunnel Josephson junctions that can be grown or processed at elevated temperatures. Also elevated synthesis temperatures improve the structural and electrical properties of Nb electrode layers that could potentially improve junction device performance. The refractory nature of Hf, HfO2 and Nb allow for the formation of flat, abrupt and thermally-stable interfaces. But the current Al-based barrier will have problems when using with high-temperature grown and high-quality Nb. So our work is aimed at using Nb grown at elevated temperatures to fabricate thermally stable Josephson tunnel junctions. As a junction barrier metal, Hf was studied and compared with the traditional Al-barrier material. We have proved that Hf-HfOx is a good barrier candidate for high-temperature synthesized Josephson junction. Hf deposited at 500 °C on Nb forms flat and chemically abrupt interfaces. Nb/Hf-HfOx/Nb Josephson junctions were synthesized, fabricated and characterized with different oxidizing conditions. The results of materials characterization and junction electrical measurements are reported and analyzed. We have improved the annealing stability of Nb junctions and also used high-quality Nb grown at 500 °C as the bottom electrode successfully. Adding a buffer layer or multiple oxidation steps improves the annealing stability of Josephson junctions. We also have attempted to use the Atomic Layer Deposition (ALD) method for the growth of Hf oxide as the junction barrier and got tunneling results.
ContributorsHuang, Mengchu, 1987- (Author) / Newman, Nathan (Thesis advisor) / Rowell, John M. (Committee member) / Singh, Rakesh K. (Committee member) / Chamberlin, Ralph (Committee member) / Wang, Robert (Committee member) / Arizona State University (Publisher)
Created2013
Interactions driving the collapse of islet amyloid polypeptide: implications for amyloid aggregation
Description
Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37-residue intrinsically disordered hormone involved in glucose regulation and gastric emptying. The aggregation of hIAPP into amyloid fibrils is believed to play a causal role in type 2 diabetes. To date, not much is known about the monomeric state of hIAPP or how it undergoes an irreversible transformation from disordered peptide to insoluble aggregate. IAPP contains a highly conserved disulfide bond that restricts hIAPP(1-8) into a short ring-like structure: N_loop. Removal or chemical reduction of N_loop not only prevents cell response upon binding to the CGRP receptor, but also alters the mass per length distribution of hIAPP fibers and the kinetics of fibril formation. The mechanism by which N_loop affects hIAPP aggregation is not yet understood, but is important for rationalizing kinetics and developing potential inhibitors. By measuring end-to-end contact formation rates, Vaiana et al. showed that N_loop induces collapsed states in IAPP monomers, implying attractive interactions between N_loop and other regions of the disordered polypeptide chain . We show that in addition to being involved in intra-protein interactions, the N_loop is involved in inter-protein interactions, which lead to the formation of extremely long and stable β-turn fibers. These non-amyloid fibers are present in the 10 μM concentration range, under the same solution conditions in which hIAPP forms amyloid fibers. We discuss the effect of peptide cyclization on both intra- and inter-protein interactions, and its possible implications for aggregation. Our findings indicate a potential role of N_loop-N_loop interactions in hIAPP aggregation, which has not previously been explored. Though our findings suggest that N_loop plays an important role in the pathway of amyloid formation, other naturally occurring IAPP variants that contain this structural feature are incapable of forming amyloids. For example, hIAPP readily forms amyloid fibrils in vitro, whereas the rat variant (rIAPP), differing by six amino acids, does not. In addition to being highly soluble, rIAPP is an effective inhibitor of hIAPP fibril formation . Both of these properties have been attributed to rIAPP's three proline residues: A25P, S28P and S29P. Single proline mutants of hIAPP have also been shown to kinetically inhibit hIAPP fibril formation. Because of their intrinsic dihedral angle preferences, prolines are expected to affect conformational ensembles of intrinsically disordered proteins. The specific effect of proline substitutions on IAPP structure and dynamics has not yet been explored, as the detection of such properties is experimentally challenging due to the low molecular weight, fast reconfiguration times, and very low solubility of IAPP peptides. High-resolution techniques able to measure tertiary contact formations are needed to address this issue. We employ a nanosecond laser spectroscopy technique to measure end-to-end contact formation rates in IAPP mutants. We explore the proline substitutions in IAPP and quantify their effects in terms of intrinsic chain stiffness. We find that the three proline mutations found in rIAPP increase chain stiffness. Interestingly, we also find that residue R18 plays an important role in rIAPP's unique chain stiffness and, together with the proline residues, is a determinant for its non-amyloidogenic properties. We discuss the implications of our findings on the role of prolines in IDPs.
ContributorsCope, Stephanie M (Author) / Vaiana, Sara M (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Ros, Robert (Committee member) / Lindsay, Stuart M (Committee member) / Ozkan, Sefika B (Committee member) / Arizona State University (Publisher)
Created2013
Description
Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.
ContributorsLiu, Hao (Author) / Lindsay, Stuart M (Committee member) / Yan, Hao (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2013
Description
In this dissertation, remote plasma interactions with the surfaces of low-k interlayer dielectric (ILD), Cu and Cu adhesion layers are investigated. The first part of the study focuses on the simultaneous plasma treatment of ILD and chemical mechanical polishing (CMP) Cu surfaces using N2/H2 plasma processes. H atoms and radicals in the plasma react with the carbon groups leading to carbon removal for the ILD films. Results indicate that an N2 plasma forms an amide-like layer on the surface which apparently leads to reduced carbon abstraction from an H2 plasma process. In addition, FTIR spectra indicate the formation of hydroxyl (Si-OH) groups following the plasma exposure. Increased temperature (380 °C) processing leads to a reduction of the hydroxyl group formation compared to ambient temperature processes, resulting in reduced changes of the dielectric constant. For CMP Cu surfaces, the carbonate contamination was removed by an H2 plasma process at elevated temperature while the C-C and C-H contamination was removed by an N2 plasma process at elevated temperature. The second part of this study examined oxide stability and cleaning of Ru surfaces as well as consequent Cu film thermal stability with the Ru layers. The ~2 monolayer native Ru oxide was reduced after H-plasma processing. The thermal stability or islanding of the Cu film on the Ru substrate was characterized by in-situ XPS. After plasma cleaning of the Ru adhesion layer, the deposited Cu exhibited full coverage. In contrast, for Cu deposition on the Ru native oxide substrate, Cu islanding was detected and was described in terms of grain boundary grooving and surface and interface energies. The thermal stability of 7 nm Ti, Pt and Ru ii interfacial adhesion layers between a Cu film (10 nm) and a Ta barrier layer (4 nm) have been investigated in the third part. The barrier properties and interfacial stability have been evaluated by Rutherford backscattering spectrometry (RBS). Atomic force microscopy (AFM) was used to measure the surfaces before and after annealing, and all the surfaces are relatively smooth excluding islanding or de-wetting phenomena as a cause of the instability. The RBS showed no discernible diffusion across the adhesion layer/Ta and Ta/Si interfaces which provides a stable underlying layer. For a Ti interfacial layer RBS indicates that during 400 °C annealing Ti interdiffuses through the Cu film and accumulates at the surface. For the Pt/Cu system Pt interdiffuion is detected which is less evident than Ti. Among the three adhesion layer candidates, Ru shows negligible diffusion into the Cu film indicating thermal stability at 400 °C.
ContributorsLiu, Xin (Author) / Nemanich, Robert (Thesis advisor) / Chamberlin, Ralph (Committee member) / Chen, Tingyong (Committee member) / Smith, David (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2012